Integrated multi-omics reveals trehalose biosynthesis genes as potential targets for salt stress mitigation in soybean

Trehalose and its intermediate, trehalose-6-phosphate (T6P), play a central role in regulating carbohydrate allocation and stress responses in higher plants through trehalose biosynthesis gene family; however, their integrative regulation and genotype-specific expression remain poorly understood in soybean. Soybean ( Glycine max L.) is an important legume crop, valued for its high protein and oil content, nitrogen (N) fixation, and food security. In this study, we performed a genome-wide characterization of soybean, identifying 22 GmTPS , GmTPP , and GmTRE genes that showed strong conservation across dicots and close phylogenetic relationships to Arabidopsis homologous. Three soybean varieties, AJMERI, NARC21, and FAISAL SOY, were tested under salinity stress induced by 100, 150, and 200 mM NaCl, undergoing reduction in biomass, chlorophyll and increased phytochemicals content. FAISAL SOY maintained better traits and higher phytochemicals accumulation, suggesting comparatively higher tolerance to salt stress. Gas chromatography-mass spectrometry (GC-MS) analysis demonstrated that control plants predominantly accumulated phenolics, while salinity stress promoted the enrichment of carboxylic acids and esters, suggesting metabolic reprogramming in response to NaCl stress. Real-time PCR analysis revealed differential expression of key genes, with GmTPS1 , GmTPS8 , GmTPPA , GmTPPC , and GmTPPJ upregulated in both roots and shoots under salinity stress while GmTRE1 was upregulated under 200 mM NaCl in FAISAL SOY, highlighting its role in osmotic adjustment and metabolic regulation. Pearson correlation analysis revealed tissue specific associations between trehalose biosynthesis genes and morphophysiological and phytochemical traits under salinity stress. This integrative study identifies genetic targets and metabolic markers that may contribute for developing stress-resilient soybean varieties.